Appendix 2—table 3.
Target regions for each gene for methylation analysis
| Gene | Ensembl gene ID | Ensembl transcript ID | Assay ID | Target location | Fwd Tm | Rev Tm | % GC | Coordinates (GRCm38/mm10) |
|---|---|---|---|---|---|---|---|---|
| Akt1 | ENSMUSG00000001729 | ENSMUST00000001780 | ADS3333 | 3’ UTR | 68 | 65.5 | 31.5 | chr12:112654548–112654709 |
| Akt1 | ENSMUSG00000001729 | ENSMUST00000001780 | ADS3332 | Intron 9/Exon 10 | 68.3 | 69.8 | 38.3 | chr12:112657120–112657273 |
| Cdh11 | ENSMUSG00000031673 | ENSMUST00000075190 | ADS3308 | Intron 3 | 66.8 | 68.3 | 36.9 | chr8:102677609–102677766 |
| Cdh11 | ENSMUSG00000031673 | ENSMUST00000075190 | ADS3318 | Intron 1 | 64.1 | 69.7 | 37 | chr8:102784569–102784722 |
| Cdh11 | ENSMUSG00000031673 | ENSMUST00000075190 | ADS3307 | Promoter | 69.1 | 71.3 | 29.9 | chr8:102785456–102785649 |
| Dnmt3a | ENSMUSG00000020661 | ENSMUST00000020991 | ADS3326 | Promoter | 68.6 | 67.7 | 47.1 | chr12:3806505–3806659 |
| Dnmt3a | ENSMUSG00000020661 | ENSMUST00000020991 | ADS632 | Intron 1 | 64 | 64.7 | 32.2 | chr12:3834382–3834592 |
| Dnmt3a | ENSMUSG00000020661 | ENSMUST00000020991 | ADS3328 | Exon 6/Intron 6 | 64.7 | 64 | 31.8 | chr12:3901545–3901764 |
| Dnmt3a | ENSMUSG00000020661 | ENSMUST00000020991 | ADS3329 | Intron 6 | 66.8 | 66.1 | 25.4 | chr12:3907514–3907765 |
| Eln | ENSMUSG00000029675 | ENSMUST00000015138 | ADS3319 | Intron 16 | 67.1 | 67.9 | 47.8 | chr5:134721191–134721447 |
| Eln | ENSMUSG00000029675 | ENSMUST00000015138 | ADS3309 | Intron 7/Exon 8/Intron 8 | 64.1 | 67.4 | 37.8 | chr5:134729221–134729526 |
| Eln | ENSMUSG00000029675 | ENSMUST00000015138 | ADS024 | Promoter | 65 | 67.4 | 42.6 | chr5:134747412–134747606 |
| Foxf2 | ENSMUSG00000038402 | ENSMUST00000042054 | ADS4505 | Promoter | 63.1 | 65 | 42.5 | chr13: 31625470–31625556 |
| Foxf2 | ENSMUSG00000038402 | ENSMUST00000042054 | ADS4506 | 5-UTR | 65.1 | 64.8 | 37.9 | chr13:31625904–31626093 |
| Foxf2 | ENSMUSG00000038402 | ENSMUST00000042054 | ADS4507 | 3-Downstream | 68 | 68.9 | 28.1 | chr13:31632481–31632716 |
| Igfbp3 | ENSMUSG00000020427 | ENSMUST00000020702 | ADS5134 | 3-Downstream | 69.3 | 69.6 | 32.1 | chr11:7203969–7204208 |
| Igfbp3 | ENSMUSG00000020427 | ENSMUST00000020702 | ADS3301 | Exon 4/Intron 4 | 70.5 | 70 | 33 | chr11:7208306–7208481 |
| Igfbp3 | ENSMUSG00000020427 | ENSMUST00000020702 | ADS5133 | Intron 1 | 68.3 | 68.5 | 26.1 | chr11:7212803–7213043 |
| Igfbp3 | ENSMUSG00000020427 | ENSMUST00000020702 | ADS5132 | Promoter | 67.8 | 69.2 | 28.7 | chr11:7214210–7214499 |
| Lox | ENSMUSG00000024529 | ENSMUST00000171470 | ADS4512 | Exon 2 | 69 | 70.9 | 31.3 | chr18: 52529184–52529315 |
| Lox | ENSMUSG00000024529 | ENSMUST00000171470 | ADS4513 | Exon 4 | 65.7 | 64.8 | 28.5 | chr18:52526887–52527023 |
| Lox | ENSMUSG00000024529 | ENSMUST00000171470 | ADS4511 | Promoter | 64.7 | 66.4 | 21.2 | chr18:52530080–52530216 |
| Sox9 | ENSMUSG00000000567 | ENSMUST00000000579 | ADS796 | Promoter | 61 | 66.1 | 31.4 | chr11:112781641–112781811 |
| Sox9 | ENSMUSG00000000567 | ENSMUST00000000579 | ADS3311 | Intron 1 | 69.7 | 68.5 | 34.7 | chr11:112783358–112783605 |
| Sox9 | ENSMUSG00000000567 | ENSMUST00000000579 | ADS3310 | Exon 3 | 66.4 | 63.1 | 26.2 | chr11:112784760–112784885 |
| Src | ENSMUSG00000027646 | ENSMUST00000109533 | ADS4514 | Intron 1 | 64.8 | 65.9 | 35.9 | chr2:157423925–157424027 |
| Src | ENSMUSG00000027646 | ENSMUST00000109533 | ADS4515 | Intron 4 | 66.5 | 68.8 | 37.6 | chr2:157457351–157457520 |
| Src | ENSMUSG00000027646 | ENSMUST00000109533 | ADS4516 | Exon 14 | 65.5 | 65.6 | 33.7 | chr2:157469741–157469912 |
| Tnc | ENSMUSG00000028364 | ENSMUST00000107377 | ADS3324 | Intron 14 | 63.3 | 62.2 | 23 | chr4:63982645–63982818 |
| Tnc | ENSMUSG00000028364 | ENSMUST00000107377 | ADS3325 | Intron 14 | 62.5 | 61.6 | 20.2 | chr4:63982799–63982986 |
| Tnc | ENSMUSG00000028364 | ENSMUST00000107377 | ADS3323 | Exon 3 | 65 | 67.5 | 35.2 | chr4:64017478–64017721 |
| Tnc | ENSMUSG00000028364 | ENSMUST00000107377 | ADS3322 | Promoter | 62.7 | 63.9 | 26.7 | chr4:64047034–64047149 |
| Vegfa | ENSMUSG00000023951 | ENSMUST00000071648 | ADS3336 | 3-UTR | 67.2 | 66.9 | 32.6 | chr17:46018598–46018735 |
| Vegfa | ENSMUSG00000023951 | ENSMUST00000071648 | ADS3335 | Intron 2/Exon 3 | 64.6 | 63.8 | 29.5 | chr17:46025336–46025620 |
| Wif1 | ENSMUSG00000020218 | ENSMUST00000020439 | ADS3302 | Promoter | 69.4 | 68.7 | 31.3 | chr10:121033395–121033691 |
| Wif1 | ENSMUSG00000020218 | ENSMUST00000020439 | ADS3303 | Intron 4/Exon 5/Intron 5 | 60.9 | 60.1 | 31.8 | chr10:121083800–121083997 |
| Wif1 | ENSMUSG00000020218 | ENSMUST00000020439 | ADS3304 | Exon 10/3-UTR | 66.6 | 67.5 | 24.8 | chr10:121099752–121099973 |
| Zfp536 | ENSMUSG00000043456 | ENSMUST00000056338 | ADS4510 | 3-Downstream | 65.4 | 67.4 | 35.9 | chr7:37473451–37473606 |
| Zfp536 | ENSMUSG00000043456 | ENSMUST00000056338 | ADS4509 | Exon 4 | 68.4 | 69.9 | 35.4 | chr7:37567973–37568130 |